Consolidate and Transcode problem

Hi,
I'm having a strange issue with a 10 minute sequence. The original media has come from many different sources, but it is all QT, albeit in various different flavours. When I project manage the sequence it looks to be fine, however, when I play it back the audio on some clips is out of sync. On some of the clips I can re-link to the audio in the project, on other clips it still re-links to the correct audio, but with incorrect in & out points.
I have tried different methods of Project Managing (altering the Source/Format/Preset drop downs) and the only box I have checked is: Exclude Unused Clips.
Here're 2 screen grabs of the first instance in the sequence where this occurred. The first is the original sequence, the second is the Project Managed version - both with the Metadata panel open. This particular version was Project Managed using the following settings:
Source: Individual Clips
Format: Quicktime
Preset: Match Source - Apple Pro Res 422 (LT)
Has anyone encountered this? Does anyone know of a work around/fix?
My system details:
Adobe Premiere Pro CC 2014 (8.2.0)
Mac Pro (Late 2013)
3.5GHz 6-core Intel Xeon E5
16GB 1866 MHz DDR3 ECC
AMD Firepro D500 3072 MB
Yosemite OSX 10.10.3
AJA ioXT v.12.2.0
Thanks in advance!

Okay,
I'm back to square one. I have tried a number of possible solutions, but nothing has worked. I either get the original synching problem outlined above, or PP links to incorrect channels.
One of my methods was to (painstakingly) convert all of the clips, create a new project, and create a new sequence:
1. Modify Clip > Audio Channels >
Preset: Mono
Channel Format: Mono
2. Create a new project. In Premiere Pro > Preferences > Audio >  select Mono as the default Audio Setting
3. Create a new Sequence and create 10 x new Mono audio tracks
4. Imported the sequence from the original project which I had converted to Mono. The audio looked the same as the original sequence (2 x channels on A1 – a Mono track), but it did at least play out as Mono – I was hoping at this stage to see mono waveforms on mono tracks.
5. Then I attempted to consolidate and transcode. No dice. The problem seems to be that one of the problematic clips (which originally had 3 x stereo pairs) is defaulting to the original stereo channel on track one. I used the audio from track two. When I convert it to mono, it’s looking at the wrong audio. This is extremely frustrating as the audio I don’t require doesn’t exist in the sequence at all! It is simply associated with the source clip.
I have a clean and split version for safety, but I really need to preserve my edit, and decrease the project size. I’m stuck…

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    RockCrab hit 9
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    RockCrab hit 4
    your health is 33
    you hit 2
    RockCrabs health is 4
    RockCrab hit 7
    your health is 26
    you hit 3
    RockCrabs health is 1
    RockCrab hit 6
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